RubyGems - genevalidator - Versions diffs - 1.6.1 → 1.6.2 - Mend

genevalidator 1.6.1 → 1.6.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (131) hide show

checksums.yaml +4 -4
data/.gitignore +3 -1
data/.travis.yml +2 -0
data/README.md +78 -30
data/Rakefile +11 -8
data/aux/app_template_footer.erb +1 -6
data/aux/app_template_header.erb +12 -32
data/aux/files/css/style.css +2 -8
data/aux/files/js/plots.js +564 -576
data/aux/files/js/script.js +10 -0
data/aux/json_footer.erb +8 -0
data/aux/json_header.erb +19 -0
data/aux/json_query.erb +14 -0
data/aux/template_footer.erb +9 -58
data/aux/template_header.erb +18 -58
data/aux/template_query.erb +8 -36
data/bin/genevalidator +45 -32
data/genevalidator.gemspec +11 -7
data/lib/genevalidator.rb +75 -455
data/lib/genevalidator/arg_validation.rb +78 -107
data/lib/genevalidator/blast.rb +57 -60
data/lib/genevalidator/clusterization.rb +15 -15
data/lib/genevalidator/exceptions.rb +32 -5
data/lib/genevalidator/get_raw_sequences.rb +70 -33
data/lib/genevalidator/hsp.rb +1 -4
data/lib/genevalidator/json_to_gv_results.rb +109 -0
data/lib/genevalidator/output.rb +177 -185
data/lib/genevalidator/pool.rb +2 -1
data/lib/genevalidator/sequences.rb +3 -3
data/lib/genevalidator/tabular_parser.rb +24 -18
data/lib/genevalidator/validation.rb +279 -0
data/lib/genevalidator/validation_alignment.rb +31 -47
data/lib/genevalidator/validation_blast_reading_frame.rb +19 -18
data/lib/genevalidator/validation_duplication.rb +23 -19
data/lib/genevalidator/validation_gene_merge.rb +30 -65
data/lib/genevalidator/validation_length_cluster.rb +14 -53
data/lib/genevalidator/validation_length_rank.rb +10 -11
data/lib/genevalidator/validation_open_reading_frame.rb +18 -19
data/lib/genevalidator/validation_report.rb +2 -5
data/lib/genevalidator/validation_test.rb +8 -4
data/lib/genevalidator/version.rb +1 -1
data/test/test_all_validations.rb +51 -66
data/test/test_blast.rb +68 -51
data/test/test_clusterization.rb +1 -1
data/test/test_clusterization_2d.rb +19 -13
data/test/test_extended_array_methods.rb +1 -1
data/test/test_files/all_validations_mrna/mrna.blast_tab6 +1806 -0
data/test/test_files/all_validations_mrna/mrna.blast_tab7 +1865 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml → mrna.blast_xml} +18642 -1
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.index → mrna.blast_xml.index} +300 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta → mrna.fa} +0 -0
data/test/test_files/all_validations_mrna/mrna.raw_seq +3970 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.raw_seq.idx → mrna.raw_seq.idx} +901 -1
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_tab → prot.blast_tab6} +416 -0
data/test/test_files/all_validations_prot/prot.blast_tab7 +2400 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml → prot.blast_xml} +18299 -6723
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.index → prot.blast_xml.index} +408 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta → prot.fa} +0 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq → prot.raw_seq} +2735 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq.idx → prot.raw_seq.idx} +3032 -1808
data/test/test_sequences.rb +46 -41
data/test/test_validation_open_reading_frame.rb +318 -202
data/test/test_validations.rb +48 -32
metadata +76 -102
data/doc/AliasDuplicationError.html +0 -134
data/doc/AlignmentValidation.html +0 -1687
data/doc/AlignmentValidationOutput.html +0 -659
data/doc/Blast.html +0 -1905
data/doc/BlastRFValidationOutput.html +0 -545
data/doc/BlastReadingFrameValidation.html +0 -370
data/doc/BlastUtils.html +0 -875
data/doc/ClasspathError.html +0 -134
data/doc/Cluster.html +0 -1316
data/doc/DuplciationValidationOutput.html +0 -564
data/doc/DuplicationValidation.html +0 -920
data/doc/DuplicationValidationOutput.html +0 -564
data/doc/FileNotFoundException.html +0 -134
data/doc/GeneMergeValidation.html +0 -935
data/doc/GeneMergeValidationOutput.html +0 -652
data/doc/HierarchicalClusterization.html +0 -994
data/doc/Hsp.html +0 -1485
data/doc/InconsistentTabularFormat.html +0 -135
data/doc/LengthClusterValidation.html +0 -982
data/doc/LengthClusterValidationOutput.html +0 -515
data/doc/LengthRankValidation.html +0 -496
data/doc/LengthRankValidationOutput.html +0 -517
data/doc/NoInternetError.html +0 -135
data/doc/NoMafftInstallationError.html +0 -134
data/doc/NoPIdentError.html +0 -134
data/doc/NoValidationError.html +0 -134
data/doc/NotEnoughHitsError.html +0 -135
data/doc/ORFValidationOutput.html +0 -593
data/doc/OpenReadingFrameValidation.html +0 -1107
data/doc/OtherError.html +0 -123
data/doc/Output.html +0 -1540
data/doc/Pair.html +0 -309
data/doc/PairCluster.html +0 -767
data/doc/Plot.html +0 -837
data/doc/QueryError.html +0 -134
data/doc/ReportClassError.html +0 -135
data/doc/Sequence.html +0 -1299
data/doc/SequenceTypeError.html +0 -135
data/doc/TabularEntry.html +0 -837
data/doc/TabularParser.html +0 -1104
data/doc/Validation.html +0 -2147
data/doc/ValidationClassError.html +0 -134
data/doc/ValidationOutput.html +0 -460
data/doc/ValidationReport.html +0 -940
data/doc/ValidationTest.html +0 -939
data/doc/_index.html +0 -449
data/doc/class_list.html +0 -54
data/doc/css/common.css +0 -1
data/doc/css/full_list.css +0 -57
data/doc/css/style.css +0 -338
data/doc/file.README.html +0 -151
data/doc/file_list.html +0 -56
data/doc/frames.html +0 -26
data/doc/index.html +0 -151
data/doc/js/app.js +0 -214
data/doc/js/full_list.js +0 -178
data/doc/js/jquery.js +0 -4
data/doc/method_list.html +0 -1505
data/doc/top-level-namespace.html +0 -112
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab +0 -967
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index +0 -967
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq +0 -4929
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx +0 -1006
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq +0 -2075
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index +0 -1864
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq +0 -42411
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq.idx +0 -3751

data/doc/OpenReadingFrameValidation.html DELETED

@@ -1,1107 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Class: OpenReadingFrameValidation
-    &mdash; Documentation by YARD 0.8.7.2
-</title>
-  <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
-  <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
-<script type="text/javascript" charset="utf-8">
-  hasFrames = window.top.frames.main ? true : false;
-  relpath = '';
-  framesUrl = "frames.html#!" + escape(window.location.href);
-</script>
-  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
-  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
-  </head>
-  <body>
-    <div id="header">
-      <div id="menu">
-    <a href="_index.html">Index (O)</a> &raquo;
-    <span class="title">OpenReadingFrameValidation</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-    <a class="full_list_link" id="class_list_link"
-        href="class_list.html">
-      Class List
-    </a>
-    <a class="full_list_link" id="method_list_link"
-        href="method_list.html">
-      Method List
-    </a>
-    <a class="full_list_link" id="file_list_link"
-        href="file_list.html">
-      File List
-    </a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: OpenReadingFrameValidation
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName"><span class='object_link'><a href="ValidationTest.html" title="ValidationTest (class)">ValidationTest</a></span></span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next"><span class='object_link'><a href="ValidationTest.html" title="ValidationTest (class)">ValidationTest</a></span></li>
-            <li class="next">OpenReadingFrameValidation</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/validation_open_reading_frame.rb</dd>
-</dl>
-<div class="clear"></div>
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-<p>This class contains the methods necessary for checking whether there is a
-main Open Reading Frame in the predicted sequence</p>
-  </div>
-</div>
-<div class="tags">
-</div>
-  <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
-  <ul class="summary">
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#filename-instance_method" title="#filename (instance method)">- (Object) <strong>filename</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute filename.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#start_codons-instance_method" title="#start_codons (instance method)">- (Object) <strong>start_codons</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute start_codons.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#stop_codons-instance_method" title="#stop_codons (instance method)">- (Object) <strong>stop_codons</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute stop_codons.</p>
-</div></span>
-</li>
-  </ul>
-  <h3 class="inherited">Attributes inherited from <span class='object_link'><a href="ValidationTest.html" title="ValidationTest (class)">ValidationTest</a></span></h3>
-  <p class="inherited"><span class='object_link'><a href="ValidationTest.html#cli_name-instance_method" title="ValidationTest#cli_name (method)">#cli_name</a></span>, <span class='object_link'><a href="ValidationTest.html#description-instance_method" title="ValidationTest#description (method)">#description</a></span>, <span class='object_link'><a href="ValidationTest.html#header-instance_method" title="ValidationTest#header (method)">#header</a></span>, <span class='object_link'><a href="ValidationTest.html#hits-instance_method" title="ValidationTest#hits (method)">#hits</a></span>, <span class='object_link'><a href="ValidationTest.html#prediction-instance_method" title="ValidationTest#prediction (method)">#prediction</a></span>, <span class='object_link'><a href="ValidationTest.html#running_time-instance_method" title="ValidationTest#running_time (method)">#running_time</a></span>, <span class='object_link'><a href="ValidationTest.html#short_header-instance_method" title="ValidationTest#short_header (method)">#short_header</a></span>, <span class='object_link'><a href="ValidationTest.html#type-instance_method" title="ValidationTest#type (method)">#type</a></span>, <span class='object_link'><a href="ValidationTest.html#validation_report-instance_method" title="ValidationTest#validation_report (method)">#validation_report</a></span></p>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#get_orfs-instance_method" title="#get_orfs (instance method)">- (Object) <strong>get_orfs</strong>(orf_length = 100, prediction = @prediction, start_codons = @start_codons, stop_codons = @stop_codons) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Find open reading frames in the original sequence Applied only to
-nucleotide sequences Params: <tt>orf_length</tt>: minimimum ORF length,
-default 100 <tt>prediction</tt>: <tt>Sequence</tt> object
-<tt>start_codons</tt>: Array of <tt>String</tt> <tt>stop_codon</tt>: Array
-of <tt>String</tt> Output: <tt>Hash</tt> containing the reading frame (the
-key) and a list of intervals (the values).</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#initialize-instance_method" title="#initialize (instance method)">- (OpenReadingFrameValidation) <strong>initialize</strong>(type, prediction, hits, filename, start_codons = [], stop_codons = []) </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Initilizes the object Params: <tt>type</tt>: type of the predicted sequence
-(:nucleotide or :protein) <tt>prediction</tt>: a <tt>Sequence</tt> object
-representing the blast query <tt>hits</tt>: a vector of <tt>Sequence</tt>
-objects (usually representig the blast hits) <tt>plot_filename</tt>: name
-of the input file, used when generatig the plot files
-<tt>start_codons</tt>: <tt>Array</tt> of codons <tt>stop_codons</tt>:
-<tt>Array</tt> of codons.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#plot_orfs-instance_method" title="#plot_orfs (instance method)">- (Object) <strong>plot_orfs</strong>(orfs, output = &quot;#{@filename}_orfs.json&quot;, prediction = @prediction) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Plots the resions corresponding to open reading frames Param <tt>orfs</tt>:
-<tt>Hash</tt> containing the reading frame (the key) and a list of
-intervals (the values) <tt>output</tt>: location where the plot will be
-saved in jped file format <tt>prediction</tt>: Sequence objects.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#run-instance_method" title="#run (instance method)">- (Object) <strong>run</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Check whether there is a main reading frame Output:
-<tt>ORFValidationOutput</tt> object.</p>
-</div></span>
-</li>
-    </ul>
-  <div id="constructor_details" class="method_details_list">
-  <h2>Constructor Details</h2>
-    <div class="method_details first">
-  <h3 class="signature first" id="initialize-instance_method">
-    - (<tt><span class='object_link'><a href="" title="OpenReadingFrameValidation (class)">OpenReadingFrameValidation</a></span></tt>) <strong>initialize</strong>(type, prediction, hits, filename, start_codons = [], stop_codons = [])
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Initilizes the object Params: <tt>type</tt>: type of the predicted sequence
-(:nucleotide or :protein) <tt>prediction</tt>: a <tt>Sequence</tt> object
-representing the blast query <tt>hits</tt>: a vector of <tt>Sequence</tt>
-objects (usually representig the blast hits) <tt>plot_filename</tt>: name
-of the input file, used when generatig the plot files
-<tt>start_codons</tt>: <tt>Array</tt> of codons <tt>stop_codons</tt>:
-<tt>Array</tt> of codons</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-57
-58
-59
-60
-61
-62
-63
-64
-65
-66
-67
-68
-69</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_open_reading_frame.rb', line 57</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span> <span class='lparen'>(</span><span class='id identifier rubyid_type'>type</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='comma'>,</span> <span class='id identifier rubyid_filename'>filename</span><span class='comma'>,</span> <span class='id identifier rubyid_start_codons'>start_codons</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='id identifier rubyid_stop_codons'>stop_codons</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-  <span class='kw'>super</span>
-  <span class='ivar'>@filename</span> <span class='op'>=</span> <span class='id identifier rubyid_filename'>filename</span>
-  <span class='ivar'>@start_codons</span> <span class='op'>=</span> <span class='id identifier rubyid_start_codons'>start_codons</span>
-  <span class='ivar'>@stop_codons</span> <span class='op'>=</span> <span class='id identifier rubyid_stop_codons'>stop_codons</span>
-  <span class='ivar'>@short_header</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>ORF</span><span class='tstring_end'>&quot;</span></span>
-  <span class='ivar'>@header</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Main ORF</span><span class='tstring_end'>&quot;</span></span>
-  <span class='ivar'>@description</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>Check whether there is a single main Open Reading Frame</span><span class='tstring_end'>'</span></span><span class='op'>&lt;&lt;</span>
-  <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'> in the predicted gene. Aplicable only for nucleotide queries. Meaning</span><span class='tstring_end'>'</span></span><span class='op'>&lt;&lt;</span>
-  <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>  of the output displayed: %=MAIN ORF COVERAGE. Coverage higher than 80%</span><span class='tstring_end'>'</span></span><span class='op'>&lt;&lt;</span>
-  <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'> passe the validation test.</span><span class='tstring_end'>'</span></span>
-  <span class='ivar'>@cli_name</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>orf</span><span class='tstring_end'>&quot;</span></span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-</div>
-  <div id="instance_attr_details" class="attr_details">
-    <h2>Instance Attribute Details</h2>
-      <span id=""></span>
-      <div class="method_details first">
-  <h3 class="signature first" id="filename-instance_method">
-    - (<tt>Object</tt>) <strong>filename</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute filename</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-44
-45
-46</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_open_reading_frame.rb', line 44</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_filename'>filename</span>
-  <span class='ivar'>@filename</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="start_codons-instance_method">
-    - (<tt>Object</tt>) <strong>start_codons</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute start_codons</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-45
-46
-47</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_open_reading_frame.rb', line 45</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_start_codons'>start_codons</span>
-  <span class='ivar'>@start_codons</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="stop_codons-instance_method">
-    - (<tt>Object</tt>) <strong>stop_codons</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute stop_codons</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-46
-47
-48</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_open_reading_frame.rb', line 46</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_stop_codons'>stop_codons</span>
-  <span class='ivar'>@stop_codons</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="get_orfs-instance_method">
-    - (<tt>Object</tt>) <strong>get_orfs</strong>(orf_length = 100, prediction = @prediction, start_codons = @start_codons, stop_codons = @stop_codons)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Find open reading frames in the original sequence Applied only to
-nucleotide sequences Params: <tt>orf_length</tt>: minimimum ORF length,
-default 100 <tt>prediction</tt>: <tt>Sequence</tt> object
-<tt>start_codons</tt>: Array of <tt>String</tt> <tt>stop_codon</tt>: Array
-of <tt>String</tt> Output: <tt>Hash</tt> containing the reading frame (the
-key) and a list of intervals (the values)</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_open_reading_frame.rb', line 122</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_get_orfs'>get_orfs</span><span class='lparen'>(</span><span class='id identifier rubyid_orf_length'>orf_length</span> <span class='op'>=</span> <span class='int'>100</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span> <span class='op'>=</span> <span class='ivar'>@prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_start_codons'>start_codons</span> <span class='op'>=</span> <span class='ivar'>@start_codons</span><span class='comma'>,</span> <span class='id identifier rubyid_stop_codons'>stop_codons</span> <span class='op'>=</span> <span class='ivar'>@stop_codons</span><span class='rparen'>)</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_type'>type</span> <span class='op'>!=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>nucleotide</span><span class='tstring_end'>&quot;</span></span>
-    <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>-</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_seq'>seq</span> <span class='op'>=</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span>
-  <span class='id identifier rubyid_len'>len</span> <span class='op'>=</span> <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-  <span class='id identifier rubyid_stops'>stops</span> <span class='op'>=</span> <span class='lbrace'>{</span><span class='rbrace'>}</span>
-  <span class='id identifier rubyid_stop_codons'>stop_codons</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_codon'>codon</span><span class='op'>|</span>
-    <span class='id identifier rubyid_occurences'>occurences</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='int'>0</span> <span class='op'>..</span> <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='int'>1</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_find_all'>find_all</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_seq'>seq</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='op'>==</span> <span class='id identifier rubyid_codon'>codon</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='rbrace'>}</span>
-    <span class='id identifier rubyid_occurences'>occurences</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_occ'>occ</span><span class='op'>|</span>
-      <span class='id identifier rubyid_stops'>stops</span><span class='lbracket'>[</span><span class='id identifier rubyid_occ'>occ</span> <span class='op'>+</span> <span class='int'>3</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_codon'>codon</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_result'>result</span> <span class='op'>=</span> <span class='lbrace'>{</span><span class='rbrace'>}</span>
-  <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-  <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='int'>2</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-  <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='int'>3</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-  <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-  <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>2</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-  <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>3</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-  <span class='comment'>#direct strand
-</span>  <span class='comment'>#reading frame 1, direct strand
-</span>  <span class='id identifier rubyid_m3'>m3</span> <span class='op'>=</span> <span class='id identifier rubyid_stops'>stops</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>0</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_sort'>sort</span>
-  <span class='id identifier rubyid_m3'>m3</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='int'>1</span><span class='comma'>,</span> <span class='id identifier rubyid_m3'>m3</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-  <span class='lparen'>(</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3'>m3</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>0</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-         <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-      <span class='kw'>end</span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_scd'>scd</span><span class='op'>|</span>
-<span class='comment'>#          start_offset = 0
-</span><span class='comment'>#          unless i == 1
-</span>          <span class='comment'>#find the first occurence of the start codon in the prospective orf
-</span>          <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='op'>-</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='op'>-</span><span class='id identifier rubyid_orf_length'>orf_length</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_find_all'>find_all</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_seq'>seq</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='op'>==</span> <span class='id identifier rubyid_scd'>scd</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>0</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span>
-<span class='comment'>#          end
-</span>        <span class='kw'>if</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>!=</span> <span class='kw'>nil</span> <span class='kw'>and</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-          <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_start_offset'>start_offset</span><span class='comma'>,</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='comment'>#reading frame 2, direct strand
-</span>  <span class='id identifier rubyid_m3_1'>m3_1</span> <span class='op'>=</span> <span class='id identifier rubyid_stops'>stops</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>1</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_sort'>sort</span>
-  <span class='id identifier rubyid_m3_1'>m3_1</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='int'>2</span><span class='comma'>,</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-  <span class='lparen'>(</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3_1'>m3_1</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>0</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-         <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='int'>2</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-      <span class='kw'>end</span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_scd'>scd</span><span class='op'>|</span>
-        <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='op'>-</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='op'>-</span><span class='id identifier rubyid_orf_length'>orf_length</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_find_all'>find_all</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_seq'>seq</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='op'>==</span> <span class='id identifier rubyid_scd'>scd</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>1</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>!=</span> <span class='kw'>nil</span> <span class='kw'>and</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-          <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='int'>2</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_start_offset'>start_offset</span><span class='comma'>,</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='comment'>#reading frame 3, direct strand
-</span>  <span class='id identifier rubyid_m3_2'>m3_2</span> <span class='op'>=</span> <span class='id identifier rubyid_stops'>stops</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>2</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_sort'>sort</span>
-  <span class='id identifier rubyid_m3_2'>m3_2</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='int'>3</span><span class='comma'>,</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-  <span class='lparen'>(</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3_2'>m3_2</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>0</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-         <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-      <span class='kw'>end</span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_scd'>scd</span><span class='op'>|</span>
-        <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='op'>-</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='op'>-</span><span class='id identifier rubyid_orf_length'>orf_length</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_find_all'>find_all</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_seq'>seq</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='op'>==</span> <span class='id identifier rubyid_scd'>scd</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>2</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>!=</span> <span class='kw'>nil</span> <span class='kw'>and</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-           <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_start_offset'>start_offset</span><span class='comma'>,</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='comment'>#reverse strand
-</span>  <span class='id identifier rubyid_stops_reverse'>stops_reverse</span> <span class='op'>=</span> <span class='lbrace'>{</span><span class='rbrace'>}</span>
-  <span class='id identifier rubyid_seq_reverse'>seq_reverse</span> <span class='op'>=</span> <span class='const'>Bio</span><span class='op'>::</span><span class='const'>Sequence</span><span class='op'>::</span><span class='const'>NA</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_seq'>seq</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_reverse_complement'>reverse_complement</span>
-  <span class='id identifier rubyid_stop_codons'>stop_codons</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_codon'>codon</span><span class='op'>|</span>
-    <span class='id identifier rubyid_occurences'>occurences</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='int'>0</span> <span class='op'>..</span> <span class='id identifier rubyid_seq_reverse'>seq_reverse</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='int'>1</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_find_all'>find_all</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_seq_reverse'>seq_reverse</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='op'>==</span> <span class='id identifier rubyid_codon'>codon</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='rbrace'>}</span>
-    <span class='id identifier rubyid_occurences'>occurences</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_occ'>occ</span><span class='op'>|</span>
-      <span class='id identifier rubyid_stops_reverse'>stops_reverse</span><span class='lbracket'>[</span><span class='id identifier rubyid_occ'>occ</span> <span class='op'>+</span> <span class='int'>3</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_codon'>codon</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_m3'>m3</span> <span class='op'>=</span> <span class='id identifier rubyid_stops_reverse'>stops_reverse</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>0</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_sort'>sort</span>
-  <span class='id identifier rubyid_m3'>m3</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='int'>1</span><span class='comma'>,</span> <span class='id identifier rubyid_m3'>m3</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-  <span class='lparen'>(</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3'>m3</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>0</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-        <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-      <span class='kw'>end</span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_scd'>scd</span><span class='op'>|</span>
-        <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='op'>-</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='op'>-</span><span class='id identifier rubyid_orf_length'>orf_length</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_find_all'>find_all</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_seq_reverse'>seq_reverse</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='op'>==</span> <span class='id identifier rubyid_scd'>scd</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>0</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>!=</span> <span class='kw'>nil</span> <span class='kw'>and</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-          <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_m3'>m3</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_start_offset'>start_offset</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_m3_1'>m3_1</span> <span class='op'>=</span> <span class='id identifier rubyid_stops_reverse'>stops_reverse</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>1</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_sort'>sort</span>
-  <span class='id identifier rubyid_m3_1'>m3_1</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='int'>2</span><span class='comma'>,</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-  <span class='lparen'>(</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3_1'>m3_1</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>0</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-        <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>2</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-      <span class='kw'>end</span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_scd'>scd</span><span class='op'>|</span>
-        <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='op'>-</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='op'>-</span><span class='id identifier rubyid_orf_length'>orf_length</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_find_all'>find_all</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_seq_reverse'>seq_reverse</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='op'>==</span> <span class='id identifier rubyid_scd'>scd</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>1</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>!=</span> <span class='kw'>nil</span> <span class='kw'>and</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-          <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>2</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_m3_1'>m3_1</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_start_offset'>start_offset</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_m3_2'>m3_2</span> <span class='op'>=</span> <span class='id identifier rubyid_stops_reverse'>stops_reverse</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>2</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_sort'>sort</span>
-  <span class='id identifier rubyid_m3_2'>m3_2</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='int'>3</span><span class='comma'>,</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-  <span class='lparen'>(</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3_2'>m3_2</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>0</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-        <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-      <span class='kw'>end</span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_start_codons'>start_codons</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_scd'>scd</span><span class='op'>|</span>
-        <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='op'>-</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='op'>-</span><span class='id identifier rubyid_orf_length'>orf_length</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_find_all'>find_all</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_seq_reverse'>seq_reverse</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span> <span class='op'>==</span> <span class='id identifier rubyid_scd'>scd</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span> <span class='op'>%</span> <span class='int'>3</span> <span class='op'>==</span> <span class='int'>2</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>!=</span> <span class='kw'>nil</span> <span class='kw'>and</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_start_offset'>start_offset</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_orf_length'>orf_length</span>
-           <span class='id identifier rubyid_result'>result</span><span class='lbracket'>[</span><span class='op'>-</span><span class='int'>3</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='lbracket'>[</span><span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_m3_2'>m3_2</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='id identifier rubyid_len'>len</span> <span class='op'>-</span> <span class='id identifier rubyid_start_offset'>start_offset</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_result'>result</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="plot_orfs-instance_method">
-    - (<tt>Object</tt>) <strong>plot_orfs</strong>(orfs, output = &quot;#{@filename}_orfs.json&quot;, prediction = @prediction)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Plots the resions corresponding to open reading frames Param <tt>orfs</tt>:
-<tt>Hash</tt> containing the reading frame (the key) and a list of
-intervals (the values) <tt>output</tt>: location where the plot will be
-saved in jped file format <tt>prediction</tt>: Sequence objects</p>
-  </div>
-</div>
-<div class="tags">
-<p class="tag_title">Raises:</p>
-<ul class="raise">
-    <li>
-        <span class='type'>(<tt><span class='object_link'><a href="QueryError.html" title="QueryError (class)">QueryError</a></span></tt>)</span>
-    </li>
-</ul>
-</div><table class="source_code">
-  <tr>
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_open_reading_frame.rb', line 279</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_plot_orfs'>plot_orfs</span><span class='lparen'>(</span><span class='id identifier rubyid_orfs'>orfs</span><span class='comma'>,</span> <span class='id identifier rubyid_output'>output</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='ivar'>@filename</span><span class='rbrace'>}</span><span class='tstring_content'>_orfs.json</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span> <span class='op'>=</span> <span class='ivar'>@prediction</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_raise'>raise</span> <span class='const'>QueryError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_orfs'>orfs</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Hash</span>
-  <span class='id identifier rubyid_len'>len</span> <span class='op'>=</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-  <span class='id identifier rubyid_f'>f</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>w</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='lparen'>(</span><span class='id identifier rubyid_orfs'>orfs</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_elem'>elem</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>0</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_len'>len</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>black</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span> <span class='op'>+</span>
-     <span class='id identifier rubyid_orfs'>orfs</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_elem'>elem</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_orf'>orf</span><span class='op'>|</span> <span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_orf'>orf</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_orf'>orf</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>red</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_json'>to_json</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_close'>close</span>
-  <span class='kw'>return</span> <span class='const'>Plot</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+)$</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='comma'>,</span>
-                  <span class='symbol'>:lines</span><span class='comma'>,</span>
-                  <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Open reading frame with START codon</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
-                  <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
-                  <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>length</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
-                  <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Reading Frame</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
-                  <span class='int'>14</span><span class='rparen'>)</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="run-instance_method">
-    - (<tt>Object</tt>) <strong>run</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Check whether there is a main reading frame Output:
-<tt>ORFValidationOutput</tt> object</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_open_reading_frame.rb', line 76</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_run'>run</span>
-  <span class='kw'>begin</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_type'>type</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span> <span class='op'>!=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>nucleotide</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:unapplicable</span><span class='rparen'>)</span>
-      <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>NotEnoughHitsError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>&gt;=</span> <span class='int'>5</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>Exception</span> <span class='kw'>unless</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span> <span class='kw'>and</span>
-                           <span class='id identifier rubyid_hits'>hits</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span>
-    <span class='id identifier rubyid_start'>start</span> <span class='op'>=</span> <span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='id identifier rubyid_orfs'>orfs</span> <span class='op'>=</span> <span class='id identifier rubyid_get_orfs'>get_orfs</span>
-    <span class='comment'># check if longest ORF / prediction &gt; 0.8 (ok)
-</span>    <span class='id identifier rubyid_prediction_len'>prediction_len</span> <span class='op'>=</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-    <span class='id identifier rubyid_longest_orf'>longest_orf</span> <span class='op'>=</span> <span class='id identifier rubyid_orfs'>orfs</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_elem'>elem</span><span class='op'>|</span> <span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_orf'>orf</span><span class='op'>|</span> <span class='id identifier rubyid_orf'>orf</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='op'>-</span><span class='id identifier rubyid_orf'>orf</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='period'>.</span><span class='id identifier rubyid_max'>max</span>
-    <span class='id identifier rubyid_ratio'>ratio</span> <span class='op'>=</span>  <span class='id identifier rubyid_longest_orf'>longest_orf</span><span class='op'>/</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction_len'>prediction_len</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_plot1'>plot1</span> <span class='op'>=</span> <span class='id identifier rubyid_plot_orfs'>plot_orfs</span><span class='lparen'>(</span><span class='id identifier rubyid_orfs'>orfs</span><span class='rparen'>)</span>
-    <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ORFValidationOutput</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_orfs'>orfs</span><span class='comma'>,</span> <span class='id identifier rubyid_ratio'>ratio</span><span class='rparen'>)</span>
-    <span class='ivar'>@running_time</span> <span class='op'>=</span> <span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span> <span class='op'>-</span> <span class='id identifier rubyid_start'>start</span>
-    <span class='ivar'>@validation_report</span><span class='period'>.</span><span class='id identifier rubyid_plot_files'>plot_files</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_plot1'>plot1</span><span class='rparen'>)</span>
-    <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-  <span class='kw'>rescue</span>  <span class='const'>NotEnoughHitsError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Not enough evidence</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:warning</span><span class='rparen'>)</span>
-    <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-  <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='ivar'>@validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>OtherError</span>
-    <span class='kw'>return</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Unexpected error</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:error</span><span class='rparen'>)</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
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-</div>
-    <div id="footer">
-  Generated on Sat Sep 28 07:01:33 2013 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.2 (ruby-1.9.3).
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